Abstract
Engineering stochastic fluctuations of gene expression (or “noise”) is integral to precisely bias cellular-fate decisions and statistical phenotypes in both single-cell and multi-cellular systems. Epigenetic regulation has been shown to constitute a large source of noise, and thus, engineering stochasticity is deeply intertwined with epigenetics. Here, utilizing chromatin remodeling, we report that Caffeic acid phenethyl ester (CA) and Pyrimethamine (PYR), two inhibitors of BAF250a, a subunit of the Brahma-associated factor (BAF) nucleosome remodeling complex, enable differential and tunable control of noise in transcription and translation from the human immunodeficiency virus long terminal repeat promoter in a dose and time-dependent manner. CA conserves noise levels while increasing mean abundance, resulting in direct tuning of the transcriptional burst size, while PYR strictly increases transcriptional initiation frequency while conserving a constant transcriptional burst size. Time-dependent treatment with CA reveals non-continuous tuning with noise oscillating at a constant mean abundance at early time points and the burst size increasing for treatments after 5 h. Treatments combining CA and Protein Kinase C agonists result in an even larger increase of abundance while conserving noise levels with a highly non-linear increase in variance of up to 63× untreated controls. Finally, drug combinations provide non-antagonistic combinatorial tuning of gene expression noise and map a noise phase space for future applications with viral and synthetic gene vectors. Active remodeling of nucleosomes and BAF-mediated control of gene expression noise expand a toolbox for the future design and engineering of stochasticity in living systems.
Highlights
Our ability to control and engineer intracellular biological processes is hampered by stochastic gene expression resulting from the dynamic and heterogeneous cell environment
The 2-state model consists of the promoter in an OFF state, with RNA polymerase II stalled behind a nucleosome stabilized by the Brahma-associated factor (BAF) remodeling complex, and an ON state, initiated at a rate kon, in which multiple pol II are released to transcribe before the promoter decays back to the inactive state at a rate koff. kon is known as the burst frequency (F)
Transcription occurs in the ON state at a rate km, and the number of messenger RNA (mRNA) produced per activity pulse of the promoter (Ton 1⁄4 1/koff) is defined as the transcriptional burst size (B 1⁄4 km*Ton 1⁄4 km/koff)
Summary
Our ability to control and engineer intracellular biological processes is hampered by stochastic gene expression (or “noise”) resulting from the dynamic and heterogeneous cell environment. Heterogeneity resulting from multiple stochastic processes including intracellular gene expression, cell to cell signaling, and environmental factors propagates up to populations of cells, tumors, and tissue patterning.. Noise in gene expression has been studied for its sources and consequences in the decision-making of diverse organisms across all kingdoms of life.. Noise in gene expression has been studied for its sources and consequences in the decision-making of diverse organisms across all kingdoms of life.2 Most recently, these fundamentals have been modeled and applied towards the active manipulation and control of noise for biasing stochastically driven systems into a desired state. Promoter nucleosome occupancy has been linked to stochastic gene expression in eukaryotes.
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